|
| Status |
Public on Apr 23, 2021 |
| Title |
Smad1/5 Prcre_2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse uterine tissues
|
| Organism |
Mus musculus |
| Characteristics |
tissue: uterine
genotype/variation: Smad1/5 Prcre
|
| Growth protocol |
For fertility analyses, 6-week-old female mice were mated to WT males of proven fertility for 6 months and the total number of pups was quantified. Smad1flox/flox and Smad5flox/flox mice were previously generated and described. To generate Smad1/5 cKO females, female mice carrying homozygous Smad1flox/flox; Smad5flox/flox alleles were crossed to males carrying the double Smad1flox/flox; Smad5flox/flox alleles and the progesterone receptor-cre (PRcre/+). A similar breeding scheme was used to generate Acvr2aflox/flox-PRcre/+ and Acvr2bflox/flox-PRcre/+ mice using Acvr2aflox/flox and Acvr2bflox/flox mice that were generated in collaboration with Dr. Se-Jin Lee. The mice were maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background. Animal handling and experimental studies were performed following the NIH Guide for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee of Baylor College of Medicine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Uterine tissues were collected from control, Smad1/5 cKO, and Acvr2a cKO mice at 3.5dpc of pseudopregnancy and immediately snap frozen on dry ice or fixed in formalin. Mice were determined to be 3.5dpc pseudopregnant according to the levels of serum progesterone. RNA was extracted from the tissues, processed in Trizol and isolated with the Direct-zol RNA extraction kit (Zymo).
Quality control of the samples was determined by assessing the RNA Integrity Number (RIN) and then used for library preparation and sequencing. Sequencing (>20M reads per sample) was performed by Novogene Corporation (Santa Cruz, CA), on the Illumina Platform (PE150).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads in FASTQ files were mapped to mm10 whole genome using HISAT2 (Galaxy tool version 2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.2). UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.
|
| |
|
| Submission date |
Jun 17, 2020 |
| Last update date |
Apr 23, 2021 |
| Contact name |
Chad Creighton |
| E-mail(s) |
creighto@bcm.tmc.edu
|
| Organization name |
Baylor College of Medicine
|
| Department |
Biostatistics, Ducan Cancer Center
|
| Street address |
One Baylor Plaza, Mail Stop: BCM305
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE152675 |
Gene expression profiling of Smad1/5 cKO and Acvr2a cKO mice |
|
| Relations |
| BioSample |
SAMN15297675 |
| SRA |
SRX8564824 |
